Align PTS system mannose-specific EIID component; EII-M-Man; EIID-Man; Mannose permease IID component (characterized)
to candidate 17213 b3140 N-acetylgalactosamine-specific enzyme IID component of PTS (NCBI)
Query= SwissProt::P69805 (283 letters) >FitnessBrowser__Keio:17213 Length = 263 Score = 163 bits (412), Expect = 4e-45 Identities = 95/274 (34%), Positives = 159/274 (58%), Gaps = 18/274 (6%) Query: 12 KLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENNEARKQAIRRHLEF 71 ++++ DI + RS+L Q S+N+ERMQA GF ++M+P ++++Y ++ A++ +LEF Sbjct: 4 EISKKDITRLGFRSSLLQASFNYERMQAGGFTWAMLPILKKIYKDDKPGLSAAMKDNLEF 63 Query: 72 FNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVGDPIFWGTVRPVF 131 NT P + ++G+ +++EE+ N I G+KV L GP+AG+GD IFW T+ P+ Sbjct: 64 INTHPNLVGFLMGLLISMEEKGEN-----RDTIKGLKVALFGPIAGIGDAIFWFTLLPIM 118 Query: 132 AALGAGIAMSGSLLGPLLFFILFNLV---RLATRYYGVAYGYSKGIDIVKDMGGGFLQKL 188 A + + A G+LLGP+LFF ++ L+ R+ + G + G K ID V++ Q + Sbjct: 119 AGICSSFASQGNLLGPILFFAVYLLIFFLRVGWTHVGYSVGV-KAIDKVRENS----QMI 173 Query: 189 TEGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILDQLMPGLVPLLLT 248 A+ILG+ V+G L+ + H+N+ V S D T V Q D++ P ++P+ T Sbjct: 174 ARSATILGITVIGGLIASYVHINV--VTSFAIDNT--HSVALQQDFFDKVFPNILPMAYT 229 Query: 249 FACMWLLR-KKVNPLWIIVGFFVIGIAGYACGLL 281 + LR KK +P+ +I FV+ I A G+L Sbjct: 230 LLMYYFLRVKKAHPVLLIGVTFVLSIVCSAFGIL 263 Lambda K H 0.326 0.143 0.439 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 214 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 283 Length of database: 263 Length adjustment: 25 Effective length of query: 258 Effective length of database: 238 Effective search space: 61404 Effective search space used: 61404 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory